[gmx-users] Melittin in methanol...

sharada sharada at ccmb.res.in
Sat Jan 31 10:54:42 CET 2009

Hello Justin,
Thanks for the reply . I apologise for the repeat mail. The parameters are for ffG43a3 forcefield. Yes I am using the default electrotatics cutoff values as an initial run. I would change to PME method as you say. However I was wondering If r_epsilon value equals to 66 contributes to a change in the simulation or this value holds good only if reaction field is on ? 
-- Original Message --
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Sat, 31 Jan 2009 00:42:36 -0500
Subject: Re: [gmx-users] Melittin in methanol...
sharada wrote:
> rlist = 0.5
> rcoulomb = 1.4
> rvdw = 0.8
You are using cut-off electrostatics by default, so you are probably getting 
some bad artifacts (use PME instead). Also, the values of rlist, rcoulomb, and 
rvdw you are using do not correspond to those for which the Gromos96 force field 
was derived. These make no sense. Refer to the original literature for 
whichever parameter set you decided to use.
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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